A split luciferase biosensing platform for detection and imaging of chromatin loops in individual live cells

Eukaryotic cells regulate higher-order chromatin architecture, gene expression, and gene recombination via compaction of the genome into chromatin loops and topologically associating domains (TADs). While chromatin architecture has been thoroughly characterized for many eukaryotic genomes using cell-destructive techniques such as 3C-based methods, live-cell biosensing tools that can probe three-dimensional chromatin contacts in real-time are lacking. Using a dual dCas9 DNA biosensor based on a split NanoLuc luciferase reporter, we directly detected chromatin loops in live cells using luminescence quantification in a luminometer. We observed signal-to-background ratios of up to 10-fold. In addition, we directly visualized chromatin looping at the MYC TAD in live cells using high-resolution, low-light live-cell imaging. Our biosensing platform therefore provides a useful methodology for live-cell, real-time detection of known or novel loops and for monitoring looping dynamics upon alterations in cell state.